Zinc in PDB 3knv: Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2

The structure of Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2, PDB code: 3knv was solved by Q.Yin, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.80 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.669, 43.669, 284.393, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 23.9

The binding sites of Zinc atom in the Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2 (pdb code 3knv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2, PDB code: 3knv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.2 occ:1.00 ND1 A:HIS51 2.2 27.0 1.0 SG A:CYS69 2.3 28.9 1.0 SG A:CYS72 2.4 28.2 1.0 SG A:CYS49 2.4 26.6 1.0 CE1 A:HIS51 3.1 28.8 1.0 CB A:CYS69 3.2 30.2 1.0 CG A:HIS51 3.2 26.9 1.0 CB A:CYS49 3.2 27.7 1.0 CB A:CYS72 3.3 31.2 1.0 CB A:HIS51 3.5 26.6 1.0 N A:CYS72 3.6 28.6 1.0 CA A:CYS72 3.9 31.2 1.0 NE2 A:HIS51 4.2 27.8 1.0 CD2 A:HIS51 4.3 28.0 1.0 N A:HIS51 4.5 24.8 1.0 CB A:ALA71 4.5 29.7 1.0 C A:ALA71 4.6 29.0 1.0 CA A:CYS69 4.6 30.9 1.0 CA A:CYS49 4.6 26.5 1.0 CA A:HIS51 4.6 25.1 1.0 C A:CYS49 4.8 26.2 1.0 O A:CYS69 4.8 31.9 1.0 C A:CYS69 4.9 30.7 1.0 O A:HOH161 4.9 33.6 1.0 OH A:TYR53 4.9 28.2 1.0 CA A:ALA71 5.0 29.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:32.3 occ:1.00 SG A:CYS57 2.2 28.0 1.0 SG A:CYS54 2.4 23.7 1.0 SG A:CYS34 2.5 27.0 1.0 SG A:CYS37 2.5 30.0 1.0 CB A:CYS54 3.0 23.3 1.0 CB A:CYS34 3.1 26.1 1.0 CB A:CYS57 3.3 28.8 1.0 CB A:CYS37 3.4 31.2 1.0 N A:CYS37 3.8 32.1 1.0 N A:CYS54 3.8 22.4 1.0 N A:GLY18 4.0 38.1 1.0 CA A:CYS54 4.0 25.2 1.0 CA A:CYS37 4.2 31.0 1.0 CA A:GLY18 4.4 35.8 1.0 CB A:PRO17 4.6 47.2 1.0 CA A:CYS34 4.6 27.6 1.0 CA A:CYS57 4.6 27.1 1.0 CD A:PRO17 4.7 48.4 1.0 CB A:ALA36 4.8 28.5 1.0 O A:HOH222 4.8 48.8 1.0 N A:CYS57 4.8 28.4 1.0 CG A:PRO17 4.9 47.5 1.0 C A:ALA36 4.9 33.7 1.0 C A:PRO17 5.0 41.8 1.0 C A:CYS37 5.0 32.0 1.0 C A:CYS54 5.0 25.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Ring and First Zinc Finger Domains of TRAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:37.9 occ:1.00 NE2 A:HIS125 2.2 32.0 1.0 SG A:CYS129 2.4 37.0 1.0 SG A:CYS107 2.4 34.4 1.0 SG A:CYS112 2.5 38.0 1.0 CD2 A:HIS125 3.1 32.2 1.0 CB A:CYS112 3.2 41.3 1.0 CB A:CYS107 3.2 35.2 1.0 CE1 A:HIS125 3.2 32.7 1.0 CB A:CYS129 3.2 35.1 1.0 CA A:CYS129 3.9 35.0 1.0 CD A:PRO130 4.1 32.1 1.0 OG A:SER109 4.1 37.9 1.0 CB A:SER109 4.2 41.4 1.0 CG A:HIS125 4.3 33.1 1.0 ND1 A:HIS125 4.3 33.5 1.0 O A:HOH199 4.4 43.1 1.0 CB A:TRP114 4.5 35.1 1.0 CA A:CYS107 4.6 37.1 1.0 CA A:CYS112 4.6 42.4 1.0 C A:CYS129 4.7 34.3 1.0 N A:PRO130 4.7 33.4 1.0

Q.Yin, B.Lamothe, B.G.Darnay, H.Wu. Structural Basis For the Lack of E2 Interaction in the Ring Domain of TRAF2. Biochemistry V. 48 10558 2009.
ISSN: ISSN 0006-2960
PubMed: 19810754
DOI: 10.1021/BI901462E